Techniques for circuit board processing are provided. In one aspect, a method of processing a circuit board having one or more optical waveguides associated therewith is provided. The method comprises the following steps. One or more etch stop layers in proximity to the one or more waveguides are provided, at least one of the etch stop layers comprising one or more fiducials therein. From a surface of the circuit board, the one or more etch stop layers are used to selectively remove material to provide openings having a defined positioning and depth in the circuit board. A circuit board having one or more optical waveguides associated therewith is also provided.